Hi Stephen, you cannot select on values of occupancies or B-factors, but you can do for examples this (which is not exactly what you asked): - remove all atoms with non-blanc altLoc identifiers: phenix.pdbtools pdb1akg.ent keep=\"altloc\ '\ '\" - keep everything except altLoc B: phenix.pdbtools pdb1akg.ent remove="altloc B" Pavel. On 8/4/09 2:26 AM, Stephen Graham wrote:

Dear all,

Apologies if this is a dumb question, but I couldn't find the answer in the docs or by asking the googlebrain. Is there a simple way in phenix.pdbtools to strip "alternate conformations" of side chains, etc, from an input PDB file? By removing "alternate conformations" I mean I would like to keep the conformation with the highest occupancy (not necessarily denoted 'A' in the altLoc column) unless all conformations have an equal occupancy, in which case I'd arbitrarily keep conformation 'A'.

I think it should be possible by a clever atom_selection command, but the correct syntax has thus-far eluded me!

Thanks,

Stephen